Biological Sciences Newsmakers

August 2016

For BioTechniques, Janet Jansson Weighs in on Science's Ways of Unlocking Microbial Communities

Vastly ubiquitous microbial communities live on, in, and
around everything on Earth, from within the human gut to across the biggest
ocean. But they are as little known as they are vital to life, health, and the
environment. In soil alone, 99 percent of microbial species have yet to be isolated.

PNNL microbiologist Janet
K. Jansson was just quoted at length regarding the stubborn mysteries of
microbial communities, which can be good or bad for the ecosystems they
populate. "There are many unknown unknowns," she said in a
feature story released in the August issue of BioTechniques. Among nine scientists quoted or cited, she was the
most frequently heard.

Up front, the story outlined the challenges of understanding
the structure and function of microbial communities. Then it outlined in detail
the techniques researchers are using to make headway. Carrying the narrative
thread was one frontier of research in particular: biofilms, the largely
bacterial multicellular communities that colonize surfaces everywhere.

Every bacterium plays a role in these layered ecosystems,
within a diversity of chemical and physical environments. Up close, the feature
said, biofilm structures are city-like, "with water channels and skyscrapers,
mushroom shapes, or thick layers peppered with pores."

Cell by cell, even single-species biofilms are complex, so
scientists have gone beyond simple chemical analysis to a variety of tools that
help investigate the spatial and temporal relationships of these cooperating
cells.

Researchers use imaging mass spectrometry to get a
two-dimensional picture of biofilm surfaces; vibrational spectroscopy to get at
the chemistry of biofilm polymers; fluorescence microscopy to show biofilms
down to the resolution of a single cell; and something called spinning disk
confocal microscopy to examine biofilm cells up to 35 microns deep, a 10-fold
improvement over previous techniques.

But scientists, Jansson among them, want to go beyond
visualizations to explore techniques that reveal how genes and proteins work
within microbial communities. In part, that means using next-generation sequencing
(NGS), "a powerful tool for examining highly heterogeneous natural microbial
communities," the article states.

"Now sequencing isn't the bottle neck," Jansson said of NGS
and other technologies that have improved so much in her 30 years of research.
"It's interpretation of the data."

But assembling all that data from NGS and elsewhere in
meaningful ways is the challenge now, she said. Microbial diversity in soil is
especially daunting, and getting good gene assemblies is hard too. But once
science has a technique to "bin" entire microbial genomes, said Jansson, it
will be a "gamechanger."

Her recent
paper with colleagues at PNNL, spelled out in the feature, used a long-lead
technique called Moleculo to facilitate a very productive round of genetic
binning and gene re-assembly in a sampling of soils from the Kansas prairie.

Jansson and her colleagues also got attention for going
beyond metagenomics to integrate that approach with other "omics" techniques. Those
include metaproteomics and metabolomics, which another scientist speculated
would be where in the near future the microbiome field "sees the greatest
technical advances."

By the article's end, Jansson was wishing out loud she could
unravel all the metabolic pathways in just one soil-bound microbial community.
After all, she added, a better understanding of those pathways could improve
predictive models of how climate change will affect the planet's ecosystems.